Feature count tracks shall support histogram view

[mzueva]

Background

Due to #462, NGB supports featureCounts format. Currently, featureCounts tracks are displaying only in a single view type in the "Browser" - similar to genes or features. It would be convenient to support a histogram view as well - e.g. bar graph with heights proportionally to feature counts.

Approach

Add a new item to the featureCounts track header to have the ability to select a view type - Display. This item shall open a list of possible view types:

• "Features" - to display a track in the currently implemented view
• "Bar Graph" (default) - to display a track as a histogram

If the "Bar Graph" view is selected - featureCounts track shall be displayed as a histogram:

• for each interval from the original featureCounts file - the own bar should be drawn. Bar height in each position shall be proportional to the value of read counts in this position
• when hovering such histogram, the tooltip shall appear that contains feature count in this position
• name of the source SAM/BAM file, used as the input for the featureCounts file, shall be displayed in the left-upper corner of the track

Example:

In case when the origin featureCounts file has several source SAM/BAM files used as the input:

• at the track, several sub-tracks shall appear - a single sub-track for each source SAM/BAM file
• each sub-track shall contain:
  • no separate header
  • name of the source SAM/BAM file in the left-upper corner of the sub-track
• when hovering such histogram, the tooltip shall appear that contains feature count in this position for the certain source SAM/BAM file
• sub-tracks shall support drag-and-drop moving (in limits of the parent track)

Example for the featureCounts track with 3 read counts sources:

Example for the featureCounts track with 2 read counts sources and zoomed-out:

Note: on big scales with "Bar Graph" mode, to not confuse users we shall show only info message like "Zoom in to see features" (default zoom level threshold should be 10m bp).

Additionally, only in case of multi-inputs, the item "Sources" shall appear in the track header. User shall have the ability to click this item to select source SAM/BAM files to show as sub-tracks. By default, all sources (sub-tracks) shall be displayed:

• if user unselects any item in this list - the corresponding sub-track shall be hidden. If user selects any item in this list - the corresponding sub-track shall appear (in limits of the parent track)
• there shall not be the ability to unselect all sources
• if user changes the view of the track to "Features" and then to "Bar Graph" - all sub-tracks should appear (no matter if they were unset previously)

Notes:

• if there are several featureCounts tracks are selected - in the common menu, the item "Sources" shall not appear
• in the "Features" display mode, item "Sources" shall not be shown in any case

Other options

For the histogram view:

• Color scheme:
  • if there are several sources of read counts - user shall have the ability to select a color scheme in which values of different sources are being colored in different colors
  • user shall have the ability to change a color scheme to "grayscale". For the single source of read counts - it should be a simple grey color, for several inputs (sources) - different tones of grey color for different sources
  • by default, the single color scheme should be set ("grayscale" mode should be disabled as well)
  • color scheme settings should be placed to the Display menu of the featureCounts track as well
• "Scale" item in the track header should appear. Via this item, users shall have the ability to configure the scale for the histogram displaying. All settings should be the same as for the WIG tracks, e.g. (see #333 for details). The only difference is that on the form for manual scale there should be only the following additional options:
  • "Apply to current track"
  • "Apply to all featureCounts tracks"
• rulers with the "key" values at Y-axis should be shown (e.g. half or third and two thirds) - as for the WIG tracks as well

[mzueva]

@rodichenko Some minor improvements:

• fix track style (same as Wig)
• shift multiselect for collapsed view is not working
• group scale overflows legend

[NShaforostov]

@rodichenko another minor improvement: When user opens the Manual scale pop-up (in the Bar Graph display mode):

• if there were any displayed bars - in the pop-up, to the field From should be set 0, to the field To should be set maximal value from all currently displayed bars
• if there were not any displayed bars - in the pop-up, fields From and To should be empty (current behavior)

[Tatyana2022]

Bug was found: The checkbox setting for the "Log scale" field is not saved in Manual scale

Prerequisites

1. Go to NGB
2. Select SV_Sample_1.byGTF.featureCounts file in SV_Sample1 dataset
3. Go to GENES panel
4. Find gene with kras name using filter
5. Click on found kras gene

Steps to reproduce:

1. Go to Browser panel
2. Go to Feature_Counts track in Browser panel from Prerequisite
3. Select Bar Graph in Displays menu(if not select)
4. Select Manual scale in Scale menu (if not select)
5. Set checkbox in Log scale field
6. Click Save button
7. Reopen Manual Scale

Expected result: The checkbox is set to the Log scale field. Actual result: The checkbox is not set to the Log scale field. Extra Details: The checkbox is not set to the Log scale field in the Displays menu also

@rodichenko

Verified

[Tatyana2022]

Bug was found: An error is displayed in the console when selected any one source and Log scale in multi track

Prerequisites: Open Console (F12)

Steps to reproduce:

1. Go to NGB
2. Go to DATASETS panel
3. Select SV_Sample_multi.featureCounts file in SV_Sample1 dataset
4. Go to BROWSER panel
5. Set CHR 5: 31387327 - 31545365 coordinates
6. Go to Feature_Counts track
7. Set Bar Graph display (if not set)
8. Set Log Scale display (if not set)
9. Uncheck any one source (e.g. **sv_sample_1.bam)
10. Look at console

Expected result: No errors in the console Actual result: An error displays in the console: app.bundle.js:514 Uncaught TypeError: Cannot read properties of null (reading 'height') at Sprite.get (app.bundle.js:514) at CoordinateSystem.value (app.bundle.js:1025) at BarChartSourceRenderer.value (app.bundle.js:1025) at app.bundle.js:1024 at Array.forEach (<anonymous>) at FCBarChartRenderer.value (app.bundle.js:1024) at FCBarChartRenderer.value (app.bundle.js:729) at FCBarChartRenderer.value (app.bundle.js:1024) at FeatureCountsTrack.value (app.bundle.js:1023) at FeatureCountsTrack.value (app.bundle.js:717)

Screenshots:

@mzueva @rodichenko

Verified

[Tatyana2022]

Bug was found: Unable to uncheck a "Features" display

Prerequisites: Dataset = sv_sample1 File = sv_sample_1.byGTF.featureCounts

Steps to reproduce:

1. Go to NGB
2. Go to DATASETS panel
3. Select dataset and file from Prerequisites
4. Go to GENES panel
5. Find gene with kras gene name
6. Click on found gene
7. Go to Feature_Counts track on BROWSER
8. Set Features display (if not set)
9. Click one more time on Features checkbox

Expected result: Features display should be unchecked. Bar Graph display should be selected automatically Actual result: Features display is still selected. Extra details: The Features checkbox is unchecked only after switching to the Bar graph display

@mzueva @rodichenko

Verified

[rodichenko]

@Tatyana2022

Bug was found: An error is displayed in the console when selected any one source and Log scale in multi track

and

Bug was found: Unable to uncheck a "Features" display

should be fixed by #595 and 8f1b3b5

Fixed

[NShaforostov]

Docs were added via #566 and located here.